Background: Previous studies on vaccination coverage in developing countries focus on individual- and community-level barriers to routine vaccination mostly in rural settings. This paper examines health system barriers to childhood immunisation in urban Kampala Uganda. Methods: Mixed methods were employed with a survey among child caretakers, 9 focus group discussions (FGDs), and 9 key informant interviews (KIIs). Survey data underwent descriptive statistical analysis. Latent content analysis was used for qualitative data. Results: Of the 821 respondents in the survey, 96% (785/821) were mothers with a mean age of 26 years (95% CI 24–27). Poor geographical access to immunisation facilities was reported in this urban setting by FGDs, KIIs and survey respondents (24%, 95% CI 21–27). This coupled with reports of few health workers providing immunisation services led to long queues and long waiting times at facilities. Consumers reported waiting for 3–6 hours before receipt of services although this was more common at public facilities. Only 33% (95% CI 30–37) of survey respondents were willing to wait for three or more hours before receipt of services. Although private-for-profit facilities were engaged in immunisation service provision their participation was low as only 30% (95% CI 27–34) of the survey respondents utilised these facilities. The low participation could be due to lack of financial support for immunisation activities at these facilities. This in turn could explain the rampant informal charges for services in this setting. Charges ranged from US$ 0.2 to US$4 and these were more commonly reported at private (70%, 95% CI 65–76) than at public (58%, 95% CI 54–63) facilities. There were intermittent availability of vaccines and transport for immunisation services at both private and public facilities. Conclusions: Complex health system barriers to childhood immunisation still exist in this urban setting; emphasizing that even in urban areas with great physical access, there are hard to reach people. As the rate of urbanization increases especially in sub-Saharan Africa, governments should strengthen health systems to cater for increasing urban populations.